ImportPathway: Process siganling pathway data

In mkarikom/RSoptSC: Low-Rank Factorization for Subspace-clustering

Process siganling pathway data

Description

Given two tsv tables, one including ligand-receptor pairs, and the other including receptor-target pairs, and a data set, inner-join the two tables and make sure no ligands, receptors, or targets are missing from the data. This function returns a summary table of all requested markers. If the data is a subset of some larger study, genes may be reported (a column exists in the data matrix) for which zero copies were observed. In this case, "dropout in subset" applies. There are also known gene symbols which were not measured in the study (no corresponding row exists in the data matrix). In this case, "missing from all subsets" applies.

Usage

ImportPathway(
  lig_table = NULL,
  rec_table = NULL,
  lig_table_path,
  rec_table_path = NULL,
  data,
  gene_names = NULL
)

Arguments

lig_table	a data frame with "ligand" in column 1 and "receptor" in column 2
rec_table	a data frame with "receptor" in column 1, "target" in column 2, and up/down "direction"
lig_table_path	a tsv/csv file with "ligand" in column 1 and "receptor" in column 2
rec_table_path	a tsv/csv file with "receptor" in column 1, "target" in column 2, and up/down "direction" in column 3
data	a matrix of the data, with gene names as row names (required if no gene list provided)
gene_names	an optional list of gene names (required if rownames of data are null)

Value

a list containing:

lignames	vector of all ligands
recnames	vector of all receptors
targets	vector of all targets
pathway	a table with combined pathway information
pathway_removed	a table with markers excluded
removed	a table with the excluded markers

mkarikom/RSoptSC documentation built on May 10, 2023, 1:10 a.m.